Manual merge for provenance visualization.

refinery-platform · Dec 29, 2014 · 12e27dd · 12e27dd
1 parent 08335d6
commit 12e27dd
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Showing 8 changed files with 2,448 additions and 2,868 deletions.
diff --git a/refinery/templates/core/data_set.html b/refinery/templates/core/data_set.html
@@ -678,7 +678,6 @@ <h3 id="myModalLabel">Launch IGV</h3>
   <!-- provenance visualization -->
 <script type="text/javascript" src="{{ STATIC_URL }}js/provvis_decl.js"></script>
 <script type="text/javascript" src="{{ STATIC_URL }}js/provvis_init.js"></script>
-<script type="text/javascript" src="{{ STATIC_URL }}js/provvis_layout_old.js"></script>
 <script type="text/javascript" src="{{ STATIC_URL }}js/provvis_layout.js"></script>
 <script type="text/javascript" src="{{ STATIC_URL }}js/provvis_render.js"></script>
 <script type="text/javascript" src="{{ STATIC_URL }}js/provvis.js"></script>

diff --git a/refinery/ui/src/js/provvis.js b/refinery/ui/src/js/provvis.js
diff --git a/refinery/ui/src/js/provvis_decl.js b/refinery/ui/src/js/provvis_decl.js
@@ -143,18 +143,30 @@ var provvisDecl = function () {
         this.x = 0;
         this.y = 0;
 
+        /* Layout specific. */
+        this.l = {
+
+            /* Top sort marking [Kahn 1962]. */
+            ts: {removed: false},
+
+            /* Graph attributes. */
+            width: 0,
+            depth: 0,
+            grid: [],
+
+            rowBK: {left: -1, right: -1},
+            bcOrder: -1,
+            isBlockRoot: false
+        };
+
         BaseNode.numInstances = (BaseNode.numInstances || 0) + 1;
         this.autoId = BaseNode.numInstances;
 
         this.doi = new DoiComponents(this);
         this.selected = false;
         this.filtered = true;
-
-        /* TODO: Group layout specific properties into sub-property. */
     };
 
-    /* TODO: Add enums for node appearance, eg.: hide, blend, lod0-2 */
-
     /**
      * Constructor function for the node data structure.
      *
@@ -187,10 +199,6 @@ var provvisDecl = function () {
         this.fileUrl = fileUrl;
 
         this.attributes = d3.map();
-
-        this.rowBK = {left: -1, right: -1};
-        this.bcOrder = -1;
-        this.isBlockRoot = false;
     };
 
     Node.prototype = Object.create(BaseNode.prototype);
@@ -223,6 +231,8 @@ var provvisDecl = function () {
         this.inputs = d3.map();
         this.outputs = d3.map();
         this.links = d3.map();
+
+        this.wfName = "";
     };
 
     Analysis.prototype = Object.create(BaseNode.prototype);
@@ -247,8 +257,6 @@ var provvisDecl = function () {
         this.outputs = d3.map();
         this.links = d3.map();
         this.isOutputAnalysis = false;
-
-        /* TODO: Workflow field. */
     };
 
     Subanalysis.prototype = Object.create(BaseNode.prototype);
@@ -303,9 +311,10 @@ var provvisDecl = function () {
      * @param color
      * @param graph
      * @param supportView
+     * @param cell
      * @constructor
      */
-    var ProvVis = function (parentDiv, zoom, data, url, canvas, nodeTable, rect, margin, width, height, radius, color, graph, supportView) {
+    var ProvVis = function (parentDiv, zoom, data, url, canvas, nodeTable, rect, margin, width, height, radius, color, graph, supportView, cell) {
         this._parentDiv = parentDiv;
         this.zoom = zoom;
         this._data = data;
@@ -321,6 +330,7 @@ var provvisDecl = function () {
         this.color = color;
         this.graph = graph;
         this.supportView = supportView;
+        this.cell = cell;
     };
 
     /**
@@ -329,6 +339,7 @@ var provvisDecl = function () {
      * @param dataset
      * @param nodes
      * @param links
+     * @param aLinks
      * @param iNodes
      * @param oNodes
      * @param aNodes
@@ -338,15 +349,13 @@ var provvisDecl = function () {
      * @param analysisData
      * @param workflowData
      * @param nodeData
-     * @param width
-     * @param depth
-     * @param grid
      * @constructor
      */
-    var ProvGraph = function (dataset, nodes, links, iNodes, oNodes, aNodes, saNodes, analysisWorkflowMap, nodeMap, analysisData, workflowData, nodeData, width, depth, grid) {
+    var ProvGraph = function (dataset, nodes, links, aLinks, iNodes, oNodes, aNodes, saNodes, analysisWorkflowMap, nodeMap, analysisData, workflowData, nodeData) {
         this.dataset = dataset;
         this.nodes = nodes;
         this.links = links;
+        this.aLinks = aLinks;
         this.iNodes = iNodes;
         this.oNodes = oNodes;
         this.aNodes = aNodes;
@@ -358,9 +367,12 @@ var provvisDecl = function () {
         this.workflowData = workflowData;
         this.nodeData = nodeData;
 
-        this.width = width;
-        this.depth = depth;
-        this.grid = grid;
+        /* Layout specific. */
+        this.l = {
+            width: 0,
+            depth: 0,
+            grid: []
+        };
     };
 
     /*    */

diff --git a/refinery/ui/src/js/provvis_init.js b/refinery/ui/src/js/provvis_init.js
@@ -1,5 +1,3 @@
-/* TODO: Add a "Reset layout" to the toolbar. */
-
 /**
  * Module for init.
  */
@@ -9,6 +7,7 @@ var provvisInit = function () {
     var dataset = Object.create(null),
         nodes = [],
         links = [],
+        aLinks = [],
         iNodes = [],
         oNodes = [],
         aNodes = [],
@@ -107,7 +106,7 @@ var provvisInit = function () {
     var extractLinks = function () {
         var lId = 0;
 
-        nodes.forEach(function (n, i) {
+        nodes.forEach(function (n) {
             if (typeof n.uuid !== "undefined") {
                 if (typeof n.parents !== "undefined") {
 
@@ -394,9 +393,14 @@ var provvisInit = function () {
         /* Set links for subanalysis. */
         saNodes.forEach(function (san) {
             links.filter(function (l) {
-                return l !== null && san.parent.uuid === l.target.analysis && l.target.subanalysis === san.subanalysis;
+                return l !== null && san.parent.uuid === l.source.analysis && l.source.subanalysis === san.subanalysis;
             }).forEach(function (ll) {
-                san.links.set(ll.autoId, ll);
+                if (san.parent.uuid === ll.target.analysis) {
+                    san.links.set(ll.autoId, ll);
+                } else {
+                    /* Set links between two analyses. */
+                    aLinks.push(ll);
+                }
             });
         });
 
@@ -418,6 +422,10 @@ var provvisInit = function () {
                 /* Set subanalysis wfUuid. */
                 san.wfUuid = an.wfUuid;
             });
+
+            /* Set workflow name. */
+            var wfObj = workflowData.get(an.wfUuid);
+            an.wfName = (typeof wfObj === "undefined") ? "dataset" : wfObj.name;
         });
 
         aNodes.forEach(function (an) {
@@ -441,7 +449,7 @@ var provvisInit = function () {
             });
         });
 
-        /* Set links. */
+        /* Set analysis links. */
         aNodes.forEach(function (an) {
             an.children.values().forEach(function (san) {
                 san.links.values().forEach(function (sanl) {
@@ -465,7 +473,6 @@ var provvisInit = function () {
         });
     };
 
-    /* TODO: Only extract attributes relevant to the filter attributes. */
     /**
      * Temporarily facet node attribute extraction.
      * @param solrResponse Facet filter information on node attributes.
@@ -547,6 +554,16 @@ var provvisInit = function () {
         $("#prov-ctrl-visible-attribute-list-name").find("input").prop("checked", true);
     };
 
+    /**
+     * Sets the parent objects for analysis nodes.
+     * @param graph The provenance graph.
+     */
+    var setAnalysisParent = function (graph) {
+        graph.aNodes.forEach(function (an) {
+            an.parent = graph;
+        });
+    };
+
     /**
      * Main init module function.
      * @param data Dataset holding the information for nodes and links.
@@ -585,7 +602,12 @@ var provvisInit = function () {
         createFacetNodeAttributeList(solrResponse);
 
         /* Create graph. */
-        return new provvisDecl.ProvGraph(dataset, nodes, links, iNodes, oNodes, aNodes, saNodes, analysisWorkflowMap, nodeMap, analysisData, workflowData, nodeData, 0, 0, []);
+        var graph = new provvisDecl.ProvGraph(dataset, nodes, links, aLinks, iNodes, oNodes, aNodes, saNodes, analysisWorkflowMap, nodeMap, analysisData, workflowData, nodeData);
+
+        /* Set parent objects for analysis nodes. */
+        setAnalysisParent(graph);
+
+        return graph;
     };
 
     /**